A Cell-Free Stock of Simian–Human Immunodeficiency Virus That Causes AIDS in Pig-Tailed Macaques Has a Limited Number of Amino Acid Substitutions in Both SIVmacand HIV-1 Regions of the Genome and Has Altered Cytotropism

AbstractWe have examined both the sequence changes in the LTR,gag, vif, vpr, vpx, tat, rev, vpu, env,andnefgenes and the cell tropism of a cell-free stock of chimeric simian–human immunodeficiency virus (SHIV) isolated from the cerebrospinal fluid of a pig-tailed macaque (PNb) that developed AIDS. This virus (SHIVKU-1) is highly pathogenic when inoculated into other macaques. DNA sequence analysis of PCR-amplified products revealed a total of 5 nucleotide changes in the LTR whilevifhad 2 consensus amino acid changes. Thegag, vif,andvpxhad no consensus amino acid substitutions, whereasvprhad 1 consensus substitution. Thetatandrevgenes of the HXB2 region of SHIVKU-1had 2 and 1 consensus amino acid changes, respectively. Thevpugene of the HXB2 region of SHIV, which originally had an ACG codon at the beginning of the gene, reverted to an initiation ATG codon and in addition contained a consensus amino acid substitution at position 69 of this protein. As expected, the majority of the nucleotide substitutions were found in theenvandnefgenes. Thirteen and 5 amino acid changes were predicted for the corresponding Env and Nef proteins, respectively. In addition, one-third of theenvgene clones isolated from the SHIVKU-1stock had a 5-amino-acid deletion in the V4 region. Using three independent assays, we determined that the changes in the SHIVKU-1were associated with an increase in the efficiency of replication in macrophages. The strikingly few consensus changes in the virus suggest that conversion of this virus to one capable of causing AIDS in pig-tailed macaques was associated with relatively few changes in the viral envelope and/or accessory genes. These results will provide the basis for the development of a pathogenic, molecular clone of SHIV capable of causing AIDS in pig-tailed macaques